Hi Vojtěch,

On Wed, Apr 26, 2017 at 1:09 PM, Vojtěch Zeisek <vo...@trapa.cz> wrote:

> Hi,
> thank You for the advice. I tried:
> densiTree(x=hirta, type="phylogram", scaleX=TRUE, width=2,
> col=rainbow(length(hirta)), font=3, underscore=FALSE)
> looks relatively nicely. I just wonder why last 2 options have no effect
> (i.e.
> I wish tip labels in italics and without underscore).


you are right the last 2 options have no effect, at least in the CRAN
version,
I added them and a few more on the in the development version on github:
devtools::install_github("KlausVigo/phangorn")



> I also didn't find how
> to add little vertical offset among trees to show identical lines in
> parallel.
>

I thought this would be your little homework, but Liam spoiled it ;) and
did all the work for you.
The densiTree function is just about 40 lines, so it would be easy just add
some offset, etc.
and I always look forward to pull requests.

Cheers,
Klaus


> Without it, the display is very messy and unreadable... :-(
> Sincerely,
> V.
>
> Dne úterý 25. dubna 2017 23:04:01 CEST jste napsal(a):
> > Hi Vojtěch,
> > you could try adopt densiTree() in phangorn to do this. It just plots
> each
> > tree separate over each other. You probably want to of move each tree a
> bit
> > up or down and add some more control for colors. It is based on the
> > internal function of from plot.phylo().
> > Cheers,
> > Klaus
> >
> > On Tue, Apr 25, 2017 at 2:25 PM, Liam J. Revell <liam.rev...@umb.edu>
> wrote:
> > > Hi Vojtěch.
> > >
> > > This kind of plot is possible to make using plotTree in phytools via
> the
> > > arguments tips (which sets the vertical coordinates of the tips,
> > > regardless
> > > of topology) & add (a logical value indicating whether to add the tree
> > > tree
> > > to an existing plot or to open a new plot). (All arguments for plotTree
> > > are
> > > documented in the man page for plotSimmap which plotTree uses
> internally.)
> > > Unfortunately, there is some complication. For instance, unless we set
> > > xlim
> > > & ylim, then plotTree will reset these values for each new plotted
> tree.
> > >
> > > Later this evening I will do my best to make an example & post it to my
> > > blog.
> > >
> > > - Liam
> > >
> > > On 4/25/2017 12:20 PM, Vojtěch Zeisek wrote:
> > >> Hello,
> > >> for comparison of two trees I can use very nice function cophyloplot
> > >> plotting
> > >> two trees (left and right) and connecting respective nodes by lines.
> Very
> > >> nice
> > >> and convenient to read. But only for two trees. Displaying multiple
> trees
> > >> in multiple comparisons is not very convenient.
> > >> To display dozens to hundreds of trees there is densitree. Also nice,
> but
> > >> for this purpose I don't like its display.
> > >> I have several trees (~5) and I wish to compare their topologies, show
> > >> supports (at least for differing nodes) and highlight differences. I
> > >> thought
> > >> about some overlay/parallel plotting (similar to the attached image)
> > >> where
> > >> there would be complete topologies displayed and incongruences would
> be
> > >> easily
> > >> visible. It would be probably doable by plotting all separate trees by
> > >> plot.phylo and then combining and tuning the figure in some vector
> editor
> > >> (like Inkscape). But I hope there is some more automated way to do it.
> > >> :-)
> > >> Sincerely,
> > >> V.
> --
> Vojtěch Zeisek
> https://trapa.cz/en/
>
> Department of Botany, Faculty of Science
> Charles University, Prague, Czech Republic
> https://www.natur.cuni.cz/biology/botany/
>
> Institute of Botany, Czech Academy of Sciences
> Průhonice, Czech Republic
> http://www.ibot.cas.cz/en/
>
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>



-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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